I believe that the formal structure of House of Leaves can be successfully interpreted through a use of Marcuse's concept of dialectical versus positivist philosophy. Central to Marcuse's thought is the idea that positivist or analytical philosophy has failed in that it has transformed the project of philosophy into merely describing the state of the world as it is, rather than as it should be; and that dialectical, negative, or critical thought offers an alternative which opens possibilities for resistance and progressive change outside the limits of official or conventional discourse.
This idea is represented in House of Leaves first if we consider the role Zampano plays compared to that of a traditional academic. We of course know that he is self-taught and extremely eccentric, but taking a closer look at his method we can see certain elements which put him in opposition to traditional academic scholarship. Page 55, footnote 67 describes an exchange between Zampano and one of his transcribers, who criticizes his work for containing "large chunks of narrative" simply describing the Navidson film which are "inappropriate for a critical work." She says he is "writing like a freshman," and Zampano's gleeful response ("We always look for doctors but sometimes we're lucky to find a frosh") shows that he is quite happy to exist outside the conventions of the university system. His decision to include the narrative description is never explained adequately (later footnotes purporting to explain it only refer back to footnote 67), but one possible reason may be that Zampano simply knew that he was writing about an imaginary film. There are several bits of evidence for this: the fact that Johnny Truant can't find evidence for the film despite Zampano emphasizing several times that it was a major studio-released blockbuster widely discussed by critics and celebrities alike, the fact that Zampano was "blind as a bat" and therefore couldn't have viewed the film in the first place, and the fact that the Editors of the book point out that the character of Navidson is "obviously based" (footnote 336, p. 368) on a real-world (our real-world, the readers') photographer. Is it then too far off to speculate that Zampano is acting as a radical philosopher who constructs a massive work which cannot exist within the traditional university structure, and thus serves as a dialectical tool to play with and critique that structure? Even if the film is somehow "real" (in the sense that it exists as a film in the universe of the book, whether or not its contents are authentic), Zampano's decision to go beyond the film and call attention to the concept of authenticity even within his own work - especially by beginning the book with a critique of the concept of authenticity itself - shows that he is not content to sit with easy answers and merely rational judgment: he is working in a complex nest of dialectical tensions and not simply accepting that "the real is rational and that the system delivers the goods" (Marcuse, Chap. 4).
The book's system of critique is further complicated by the existence of Johnny Truant's footnotes. These exist even further outside the academic mainstream that Zampano's work, and by using Zampano over and over again as a platform from which to express his personal narrative and confess his inner demons Johnny is breaking out of the confines of positivist logic by refusing to submit to typical categories (memoir, academic criticism, literature, journal, etc.). Instead he expresses his deep unhappiness with his life and the series of tragedies and abuses he has suffered, and by injecting these personal miseries into Zampano's critical work he ties the two together: intellectual inquiry and stream-of-consciousness account of personal misery working with and against one another in order to present a whole picture of the world's failings.
The film itself, taken as a work of art in itself, also presents critical thinking in the form of its plot. Initially we see that Navidson intended for his film to be a simple record of "how people move into a place and start to inhabit it [...] Personally, I just want to create a cozy little outpost for me and my family" (Danielewski, p. 23). Zampano calls this an "innocuous and laconic rumination" but points out the militaristic connotation of Navidson's use of the word "outpost." This is an inspired bit of critical/dialectical thinking on Zampano's part - his attention to the subtleties of language would make Marcuse proud - but we can see how this plays out in the plot of the film itself, as the mysteries of the house present to us what is essentially a dark underbelly to the seemingly "innocuous" project of recording a family's relocation. We can read later events as merely using the conceit of a haunted/demonic/supernatural/etc. house to reveal the underlying tensions already present in the Navidson family: Karen's infidelity and claustrophobia originating in her abuse as a child, Navidson's possessiveness and extreme guilt over his experience with Delial, and so on. The house serves as a kind of excuse for the film to delve into the dialectical tensions which exist between Karen and Navidson, Navidson and his brother, Karen and the children, and so on, to perform an artistic critique of the positivist assertion that the family is "just" moving in and settling into a new house. It is revealing hidden, underlying, "essential" tensions which Navidson at first hopes to conceal by moving the family into a new environment.
So, we can see that on three separate levels Danielewski is presenting us with characters and situations which present a critical or dialectical account of everyday life, augmented by the conceit of a horror story within a book within a book etc., which calls attention to itself as a critique in order to more fully penetrate any totalizing positivist logic which exists in the "typical" forms of writing.